The poem
Towery city and branchy between towers; Cuckoo-echoing, bell-swarmèd, lark-charmèd, rook-racked, river-rounded; The dapple-eared lily below thee; that country and town did Once encounter in, here coped and poisèd powers; Thou hast a base and brickish skirt there, sours That neighbour-nature thy grey beauty is grounded Best in; graceless growth, thou hast confounded Rural rural keeping—folk, flocks, and flowers.
Yet ah! this air I gather and I release He lived on; these weeds and waters, these walls are what He haunted who of all men most sways my spirits to peace;
Of realty the rarest-veinèd unraveller; a not Rivalled insight, be rival Italy or Greece; Who fired France for Mary without spot.

we are studying the poetry of Scotus and need help with what the last two lines are all about?
They are about the immacolate conception of the Virgin Mary